Description Usage Arguments Value Examples
It is used to obtain the parameters of the pulse function J Comput Biol (2009 Feb) <doi:10.1089/cmb.2008.13TT>, including transcription parameters, degradation parameters and processing parameters.
You can use these parameters to analyze transcriptional characteristics, including steady-state analysis.
At the same time, you can use pulseModel
to view the curve corresponding to the parameter.
1 |
object |
a 'pulseTDmodel' that has been calculated with |
stage |
A character is one of three stages of transcriptional dynamics, transcription, processing and degradation. |
genename |
a vector, default is NULL
|
A matrix or vector containing six parameters: h0,h1,h2,t1 t2,beta
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | data('pulseRates', package='pulseTD')
TimeGrid <- c(0, 15, 30, 45, 60, 75, 90, 105, 120, 135, 150, 165, 180)
pulseRates_correct <- correctionParams(pulseRates)
transcription_params = getParams(pulseRates,'transcription')
degradation_params = getParams(pulseRates, 'degradation')
processing_params = getParams(pulseRates, 'processing')
head(transcription_params)
head(degradation_params)
head(processing_params)
transcription_params = getParams(pulseRates, 'transcription', genename=c(1,2,3))
head(transcription_params)
###
transcription_pulse = pulseModel(as.matrix(transcription_params[1,]), TimeGrid)
degradation_pulse = pulseModel(as.matrix(degradation_params[1,]), TimeGrid)
processing_pulse = pulseModel(as.matrix(processing_params[1,]), TimeGrid)
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